The improvement of host plant resistance to cotton pathogens depends upon the germplasm resources available from which genetic material can be drawn. We are fortunate that cotton has a rather large base of germplasm resources. However, the availability of genetic material varies with the species being examined. For convenience germplasm resources are grouped into primary, secondary and tertiary pools according to the ease with which the genetics can be tapped. For cotton all of the tetraploid species, including three wild species, are included in the primary pool. The secondary pool includes all species that have close homoeology to either the A or D genome of the cultivated tetraploids. This includes species in the A, B, F and D genomes. The tertiary pool is the least accessible and includes those species indigenous to Australia and those in the E genome. Strategies have been developed for efficient enhancement of the secondary germplasm pool, but the tertiary pool remains a difficult resource to utilize. Genetic engineering has opened many possibilities for improving the resistance of cotton to diseases.